Novel L-asparaginase from Paucilactobacillus vaccinostercus: Insights into anti-cancer potential using metagenomic, molecular docking and molecular dynamics simulation

Abstract

The current study presents the identification and characterization of six high-quality MAGs isolated from fermented bamboo shoots, namely Lacticaseibacillus pantheris, Enterococcus italicus, and Paucilactobacillus vaccinostercus from DBMD, Enterococcus italicus DBMK, Pediococcus pentosaceus PBMD, and Lactococcus lactis PBMA. Functional annotation revealed gene clusters associated with immune modulation, probiotic properties, and stress tolerance. Notably, all MAGs encode L-asparaginase, an enzyme with significant anticancer potential. Molecular docking analysis showed that Paucilactobacillus vaccinostercus DBMD L-asparaginase had the highest affinity toward L-asparagine (−8.5 kcal/mol), followed by Enterococcus italicus DBMD (−7.8 kcal/mol), whereas the commercial enzyme Elspar demonstrated substantially lower affinity (−4.2 kcal/mol). In-depth MD simulations over 100 ns confirmed that the L-asparaginase–L-asparagine complex from Paucilactobacillus vaccinostercus DBMD was the most stable, exhibiting a lower RMSD (0.26 ± 0.034 nm), reduced flexibility (RMSF: 0.131 nm), and tighter structural compactness (Rg: 2.047–2.059 nm) than both Enterococcus italicus DBMD and Elspar. MM-PBSA binding energy calculations further substantiated these findings, with P. vaccinostercus DBMD showing a significantly higher binding affinity (−190.28 kJ/mol) compared to Enterococcus italicus DBMD (−48.16 kJ/mol) and Elspar (−12.47 kJ/mol). These results highlight the dual potential of the identified MAGs as probiotics and anticancer agents, with the L-asparaginase from Paucilactobacillus vaccinostercus DBMD emerging as a promising therapeutic enzyme with superior performance over the commercial standard.